Gut commensal bacterium and methods of using the same

ABSTRACT

The invention provides gut commensal bacteria that have been modified to express one or more biologically active polypeptides or protiens, the bacteria includes a promoter, such as a xylanase promoter, which is induced in response to the presence of xylan in the diet and which regulates the expression of the biologically active polypeptide or protien.

RELATED APPLICATIONS

The present application is a 35 U.S.C. §371 national phase applicationof PCT International Application No. PCT/GB2006/000222, having aninternational filing date of Jan. 24, 2006 and claiming priority toGreat Britain Patent Application No. 0501540.9, filed Jan. 25, 2005, thedisclosures of which are incorporated herein by reference in theirentireties. The above PCT International Application was published in theEnglish language and has International Publication No. WO 2006/079790.

The present invention relates to the production and secretion ofbiologically active polypeptide(s) or protein(s) by gut microflora,methods of delivering same and methods of controlling the production andsecretion of said biologically active polypeptide(s) or protein(s). Thepresent invention is of particular use in the development of newimmunotherapies and especially for the treatment of inflammatory gutdiseases.

BACKGROUND

The microbial community in the human large intestine consists of adiverse range of bacteria that are predominantly obligate anaerobes.These bacteria act together to degrade dietary substrates that reach thecolon (including insulin, fructo-oligosaccharides and resistant starch),producing a range of products that are important for human health anddisease.

The mucosal immune response can be influenced by manipulation of thenormal resident bacterial flora. This flora possesses a large variety ofbiological and immunomodulatory properties that can, directly orindirectly, influence the development and function of the mucosal immunesystem. Chronic disorders of the gut, for example inflammatory boweldisease (IBD) which includes the disorders Crohn's disease andulcerative colitis, affect a significant proportion of the population indeveloped countries. Animal models of mucosal inflammation have beenused to try and determine the immune mechanisms involved in thepathogenesis of these diseases. Chronic colitis develops spontaneouslyin interleukin (IL) 2^(−/−) and IL10^(−/−) mice both of which are usedas models of IBD. Many other mouse models of IBD have also beendescribed, most of which have targeted deletions of immune responsegenes. Current treatment of IBD is restricted to anti-inflammatory andimmunosuppressive drug therapies including recombinant IL10 andantibodies to tumour necrosis factor-α (TNF-α). However, these therapiesare not curative and may cause adverse side effects such as toxicity andimmunosuppression. Therefore, there is a need for a more targeted andcontrolled form of immunotherapy.

It is known from the prior art to use commensal, or bacteria that occurnaturally in the alimentary canal, such as Lactobacillus spp. andStreptococcus spp. to treat intestinal inflammation and certain forms ofIBD in humans (Shanahan 2001), however these results have limitedevidence of success and inconsistent efficacy. It is also known from theprior art to use genetically engineered food grade Lactococcus lactis tosecrete interleukin-10 (IL10), which when administered intragastricallyto two murine models of IBD was shown to be as effective in bothpreventing and treating disease as the more conventional steroid therapy(Steidler et al. 2000). This Lactococcus system has also been used toproduce biologically active IL2 and IL6 (Steidler et al. 1995; Steidleret al. 1998). However, a major disadvantage associated with these priorart systems is that L. lactis is not able to colonise the gut due to theinability of the organism to bind to the gut epithelium and/or itsnutritional dependence on the provision of amino acids and peptideswhich are unavailable in vivo. Accordingly any in vivo treatment ortherapy would require repeated dosing to the appropriate site with themodified organism.

Another biosafety concern and disadvantage of the use of this particularaerobic bacterium is that it could survive outside of the host/patientfor sufficient time to be transmitted to others.

A yet further disadvantage of the prior art systems is that there is nomeans of controlling the constitutive expression of the immunologicallyactive interleukin molecules and these active molecules themselves whenoverproduced, can have adverse effects. Accordingly the prior artgenetically modified probiotic systems lack control and regulation ofthe activity of probiotic bacteria after administration. This representsa serious safety issue for human therapy.

To address the deficiencies in the prior art and to further developcommensal bacteria as novel delivery systems for biologically activemolecules, we have developed genetically engineered probiotic organismsin which the production of immunotherapeutic agents by commensalbacteria in situ can be regulated and controlled by dietary factors.

It is an object of the present invention to engineer a gut commensalbacterium so as to produce and secrete biologically activepolypeptide(s) or protein(s) in a regulated manner as a basis for novelimmunotherapies for chronic gut disorders.

BRIEF SUMMARY OF THE DISCLOSURE

According to a first aspect of the invention there is provided a gutcommensal bacterium deposited under the provisions of the BudapestTreaty at the National Collection of Industrial, Food and MarineBacteria (NCIMB) Ferguson Building, Craibstone Estate, Bucksburn,Aberdeen, Scotland AB21 9YA on Nov. 29, 2007 and assigned Accession No.41521 (Bacteriodes ovatus BO-KGF), 41522 (Bacteriodes ovatus BO-TGF) or41523 (Bacteriodes ovatus BO-MUIL2-S) modified to express one or morebiologically active polypeptides or proteins, the bacterium furthercomprising a promoter which is induced in response to the presence of adietary factor and which regulates the expression of said biologicallyactive polypeptide or protein.

Throughout the description and claims of this specification, the words“comprise” and “contain” and variations of the words, for example“comprising” and “comprises”, means “including but not limited to”, andis not intended to (and does not) exclude other moieties, additives,components, integers or steps.

Throughout the description and claims of this specification, thesingular encompasses the plural unless the context otherwise requires.In particular, where the indefinite article is used, the specificationis to be understood as contemplating plurality as well as singularity,unless the context requires otherwise.

Features, integers, characteristics, compounds, chemical moieties orgroups described in conjunction with a particular aspect, embodiment orexample of the invention are to be understood to be applicable to anyother aspect, embodiment or example described herein unless incompatibletherewith.

An operon may be defined as a functional unit consisting of a promoter,an operator and a number of structural genes. An example is the xylanaseoperon. The structural genes commonly code for several functionallyrelated enzymes, and although they are transcribed as one(polycistronic) mRNA, each has its separate translation initiation site.In the typical operon, the operator region acts as a controlling elementin switching on or off the synthesis of mRNA. The xylanase operon isactivated in the presence of xylan.

Preferably, the promoter is constitutive and more preferably is thexylanase promoter. Thus it will be appreciated that the expression ofthe one or more biologically active polypeptides or protiens iscontrolled by the presence of xylan in the diet. The bacteria cantherefore be said to comprise a xylan-inducible regulatory element.

Xylan is a water-soluble, gummy polysaccharide found in plant cell wallsand yielding xylose upon hydrolysis. It is therefore a common dietaryfactor or component, accordingly the inclusion or exclusion of xylan inthe diet controls the expression of the biologically active polypeptideor protien. The modified bacteria of the present invention thereforeadvantageously provide an easily controllable expression system avoidingrepeated invasive dosing of an individual since the modified bacteria ofthe present invention are also able to colonise the gut whilstconcomitantly minimising any adverse side-effects.

Preferably, the bacterium is obligate anaerobe and more preferably stillsaid bacterium is either Bacteroides ovatus or Prevotella.

Preferably, the bacterium in non-pathogenic to man.

“Biologically active” refers to the ability to perform a biologicalfunction. The biologically active polypeptide or protein used in thepresent invention can be either homologous to the bacterium orheterologous thereto, derived from either eukaryotic or prokaryotic orviral sources.

Specific examples of such polypeptides and proteins used in the presentinvention preferably include insulin, growth hormone, prolactin,calcitonin, luteinising hormone, parathyroid hormone, somatostatin,thyroid stimulating hormone, vasoactive intestinal polypeptide, trefoilfactors, cell and tissue repair factors, transforming growth factor β,keratinocyte growth factor, a structural group 1 cytokine adopting anantiparallel 4α helical bundle structure such as IL-2, IL-3, IL-4, IL-5,IL-6, IL-7, IL-9, IL-10, IL-11, IL-12, IL-13, GM-CSF, M-CSF, SCF, IFN-γ,EPO, G-CSF, LIF, OSM, CNTF, GH, PRL or IFNα/β, a structural group 2cytokine which are often cell-surface associated, form symmetrichomotrimers and the subunits take up the conformation of β-jelly rolldescribed for certain viral coat proteins such as the TNF family ofcytokines, eg TNFα, TNFβ, CD40, CD27 or FAS ligands, the IL-1 family ofcytokines, the fibroblast growth factor family, the platelet derivedgrowth factors, transforming growth factor p and nerve growth factors, astructural group 3 cytokine comprising short chain α/β molecules, whichare produced as large transmembrane pre-cursor molecules which eachcontain at least one EGF domain in the extracellular region, eg theepidermal growth factor family of cytokines, the chemokinescharacterised by their possession of amino acid sequences grouped aroundconserved cysteine residues (the C-C or C-X-C chemokine subgroups) orthe insulin related cytokines, a structural group 4 cytokine whichexhibit mosaic structures such as the heregulins or neuregulins composedof different domains, eg EGF, immunoglobulin-like and kringle domains.

Alternatively, the biologically active polypeptide can be a receptor orantagonist for biologically active polypeptides as defined above.

The bacterium expresses the biologically active polypeptide or proteinand the antigen from nucleic acid contained within it. The nucleic acidmay comprise one or more nucleic acid constructs in which nucleic acidencoding the biologically active polypeptide and nucleic acid encodingthe antigen are under control of appropriate regulatory sequences forexpression in the bacterium.

The bacterium may also express the biologically active polypeptide orprotein as a vaccine.

Preferably, the bacterium of the present invention may be modified toexpress a plurality of biologically active polypeptides or proteins.

According to a further aspect of the invention there is provided apharmaceutical comprising a gut commensal bacterium modified to expressone or more biologically active polypeptides or protiens, the bacteriumfurther comprising a promoter which is induced in response to thepresence of a dietry factor and which regulates the expression of saidbiologically active polypeptide or protien.

Preferably, the pharmaceutical is provided as a composition in aphysiologically acceptable carrier, diluent or excipient.

Preferably, the pharmaceutical comprises any one or more of the featureshereinbefore recited.

According to a further aspect of the invention there is provided use ofa gut commensal bacterium modified to express one or more biologicallyactive polypeptides or protiens, the bacterium further comprising apromoter which is induced in response to the presence of a dietry factorand which regulates the expression of said biologically activepolypeptide or protien, in the manufacture of a medicament for thetreatment of chronic infammatory bowel disease.

Preferably, the use further comprises any one or more of the featureshereinbefore recited.

According to a further aspect of the invention there is provided amethod of delivering one or more biologically active polypeptides orproteins or antigens or enzymes or vaccine which comprises administeringto a subject a gut commensal bacterium which expresses one or more ofsaid biologically active agents expression of which is under control ofa promoter which is activated in the presence of a dietry factor.

Preferably, bacterium expresses more than one biologically activepolypeptide or protein or antigen or enzyme or vaccine or a combinationthereof.

Preferably, the method comprises the administration of a mixture ofbacteria expressing a variety of biologically active polypeptides orproteins or antigens or enzymes or vaccines or a combination thereof.

Thus it will be appreciated that in this embodiment of the inventionthere is provided, for example and without limitation, bacteria capableof expressing IL2 and bacteria capable of expressing IL12 and/or IL9 andoptionally bacteria capable of expressing a cell and tissue repairfactor.

Preferably, the method includes any one or more of the features hereinbefore described.

Bacteroides ovatus, is a major commensal colonic Gram-negative bacteriumin humans and rodents for which cloning systems are available that allowthe introduction of foreign DNA into the organism and integration intothe genome (Tancula et al. 1992). This organism is also one of only afew that are able to degrade the polysaccharide xylan. We provideevidence for the successful engineering of B. ovatus to produce murineIL2 (MuIL2) intracellularly under the control of the xylanase promotorwhich is active in the presence of xylan. Our results demonstrate thatB. ovatus can be induced to produce biologically active MuIL2 inresponse to xylan. We have also engineered a second strain to secreteMuIL2 by adding the B. fragilis enterotoxin secretion signal sequence tothe protein. The recombinant strains produced MuIL2 only in the presenceof xylan as determined by enzyme-linked immunosorbent assay of celllysates and culture supernatants. The IL2-dependent cell line CTLL-2 wasused to demonstrate that MuIL2 produced by both B. ovatus strains wasbiologically active. Moreover, this activity could be blocked by ananti-IL2 neutralising antibody.

According to a further aspect of the invention there is provided amethod of treating chronic inflammation of the gut comprisingadministering to an individual suffering from such a condition apharmaceutically effective amount of a gut commensal bacterium modifiedto express one or more biologically active polypeptides or protiens, thebacterium further comprising a promoter which is induced in response tothe presence of a dietry factor and which regulates the expression ofsaid biologically active polypeptide or protien.

The use of bacteria of the invention as drug delivery vehicles offers ameans of delivering immunomodulatory factors, such as cytokines, andother biologically active molecules directly to the site action to treatchronic inflammation of the gut.

The advantages of this unique form of therapeutic delivery is that it isa convenient and simple means of delivering biologically active proteinsdirectly to their site of action, avoiding the inconvenience andsystemic exposure associated with parenteral therapy

The present invention will be described by way of example only withbrief reference only to the following Figures wherein:

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows a schematic construction of plasmid pBOMuIL2.

FIG. 2 shows a bar chart of levels of MuIL2 in cell lysates (CL) andculture supernatants (SN) of B. ovatus BOMuIL2, B. ovatus BOMuIL2-S andcontrol strains (V975 and BT2) grown with xylan for 24 h (+X) or withoutxylan.

FIG. 3 shows the result of a bioassay of MuIL2 in culture supernatantsof B. ovatus BOMuIL2-S grown with xylan.

FIG. 4 shows a gel of increased expression of MuIL2 mRNA in response toxylan determined by RT-PCR with test (BOMuIL2 and BOMuIL2-S) or controlstrains (V975 and BT2) of B. ovatus grown for 24 h in RGM without xylanfollowed by 1 h with xylan.

FIG. 5 shows the construct map of B ovatus expressing either human TGFβor KGF.

FIG. 6 A shows the production of human cytokines by B. ovatus expressinghuman TGFβ in response to xylan and FIG. 6 B shows the production ofhuman cytokines by B. ovatus expressing human KFG in response to xylan.

DETAILED DESCRIPTION

Bacterial Strains, Plasmids and General DNA Manipulations

E coli DH5α and J53/R751 were grown in LB medium. Cultures of E. coiJ53/R751 were supplemented with 200 μg trimethoprim ml⁻¹. B. ovatus V975was grown anaerobically at 37° C. in brain heart infusion (BHI) brothsupplemented with 10 μg haemin ml⁻¹ or in routine growth medium (RGM)prepared as described by Hespell et al. (1987) and supplemented with0.1% (w/v) glucose. Where xylan was required, a hot water-solublefraction of oatspelt xylan was prepared by the method of Hespell andO'Bryan (1992) and added to media at a concentration of 0.2% (w/v).Transfer of plasmids to B. ovatus from E. coli J53/R751 was carried outby conjugation as described by Valentine et al. (1992). pBT2 (Tancula etal. 1992) was selected in E. coli using 50 μg kanamycin ml⁻¹ . B. ovatustransconjugants were selected on BHI-haemin agar containing 200 μggentamicin ml⁻¹ and 5 μg tetracycline ml⁻¹. Transconjugants weresubsequently grown in medium containing 1 μg tetracycline ml⁻¹. E. coliwas transformed by the method of Hanahan (1983). General DNAmanipulations were carried out as described by Sambrook et al. (1990).

Construction of MuIL2-producing and control B. ovatus strains

MuIL2-producing strain BOMuIL2. The MuIL2 gene was PCR-amplified fromcDNA cloned in pUC13 using primers MuIL2F1 (GCGCATATGGCACCCACTTCMGCTCCAC;SEQ ID NO:1 Ndel site in bold) and MuIL2R1 (GCGGGATCCTTATTGAGGGCTTGTTGAGATGATG; SEQ ID NO:2 BamH1 site in bold). A portion ofthe B. ovatus xylanase operon encompassing the 3′ half of the orf geneand region between this gene and the xyl gene was amplified from plasmidpOX1 (Whitehead and Hespell 1990) using primers ORFF1 (GCGGGATCCATGGAGCATGAATGCGTCA; SEQ ID NO:3 BamHI site in bold) and ORFR1 (CATATGTTATATTTTTGAGTMTAAACATTCTAC; SEQ ID NO:4 Ndel site in bold). The MuIL2 andORF PCR products were cloned into pGEM-T (Promega) to create plasmidspGEM-MuIL2 and pGEM-ORF respectively. MuIL2 was removed from pGEM-MuIL2with Ndel and ligated into Ndel-digested PGEM-ORF to create pORF-MuIL2.The insert was sequenced to verify the construct. The ORF-MuIL2construct was removed from pORF-MuIL2 by BamHI digestion and cloned intothe BamHI site of pBT2 to create pBOMuIL2. This plasmid was transferredinto B. ovatus by conjugation and integration of the plasmid into thegenome of transconjugants was confirmed by PCR. MUIL2-secreting strainBOMuIL2-S. B. ovatus strain BOMuIL2-S was constructed in the same way asstrain BOMuIL2 except that the MuIL2 gene was PCR-amplified usingprimers BFTSIGIL2F (GACATATGMGAATGTAAAGTTACTTTTAATGCTAGGAACCGCGGCATTATTAGCTGCAGCACCCACTTCAAGCTCCAC; SEQ ID NO:5 signalsequence coding region is underlined, Ndel site in bold) and MuIL2R1.This led to the creation of plasmids pGEM-MuIL2-S, pORF-MuIL2-S andpBOMulL2-S.

Control strain BT2. The control strain containing pBT2 without the MuIL2gene was constructed as follows. The same portion of the off gene asused above was PCR amplified with primers ORFF1 and ORFR2(GGATCCTTATATTTTTGAGTAAT AAACATTCTAC; SEQ ID NO:6 BamHI site in bold)and cloned into pGEM-T to create pGEM-ORFB. The insert was removed withBamHI and cloned into the BamHI site of pBT2 to create pBT-ORF. Thisplasmid was transferred into B. ovatus as described above.

Preparation of Samples of B. ovatus producing MuIL2.

B. ovatus strains V975, BT2, BOMuIL2 and BOMuIL2-S were grown in 10 mlRGM with or without xylan for 24 h. Strains BOMuIL2 and BOMuIL2-S werealso grown for 16 h without xylan and then with xylan for a further 8 h.Following incubation, cells were harvested (5000 g, 30 min, 4° C.).Supernatants were removed and frozen. Cells were washed once in 10 mlRGM and resuspended in 5 ml distilled water. Cells were disrupted bysonication on ice for 4×20 sec at 12 μm (Soniprep 150, MSE). Unbrokencells and cell debris were removed by centrifugation (13,000 g, 20 min,4° C.). Lysates and supernatants were lyophilized and resuspended in 0.5ml distilled water.

Assays for Detection of MuIL2

An ELISA incorporating native rat anti-mouse IL2 (clone JES6-1A12) andbiotinylated rat anti-mouse IL2 (clone JES65H4) as capture and detectionantibodies respectively, was used to quantify levels of MuIL2 producedby recombinant strains of B. ovatus and was carried out according tomanufacturer's instructions (BD Pharmingen). Recombinant MuIL2 (rMulL2;Sigma) was used as a control to obtain a standard curve. An IL2 bioassayusing the indicator cell line CTLL-2 (Gillis et al. 1978) was used todetect the presence of biologically active MuIL2 in samples (Wadhwa etal. 2000). Briefly, cells were incubated with dilutions of test samplesor control rMuIL2 in 96-well plates in duplicate for 18 h. Cells werethen pulsed with 0.5 μCi [³H]thymidine, harvested after 4 h and theradioactivity incorporated into DNA estimated by scintillation counting.The assay was also performed in the presence of an IL2 neutralisingantibody (clone JES6-1A12). This was added to samples at a concentrationof 5 μg ml⁻¹ 1 h before addition of cells.

Detection of MuIL2 transcription by RT-PCR

B. ovatus V975, BT2, BOMuIL2 and BOMuIL2-S were grown in RGM withoutxylan for 16 h. A preinduction sample was taken from cultures of BOMuIL2and BOMuIL2-S before xylan was added to induce transcription of thexylanase operon. Samples were taken from all four cultures after 1 h.Total RNA was extracted from cell samples using the RNeasy kit (Qiagen)followed by treatment with TURBO DNA-free™ (Ambion) to remove anyresidual contaminating DNA. RT-PCR was performed using the AccessQuick™RT-PCR System (Promega) and primers for the orf-Muil2 fusion(CCGATGGTACCTGCCATTAAA (SEQ ID NO:7) and CTGTGCTTCCGCTGAGG) SEQ ID NO:8or the gyrA gene (CTCCATGTCGG TCATCGTTTC (SEQ ID NO:9) andCAAAGGATMCGCATTGCCCA (SEQ ID NO:10)) as a positive control. As anegative control the reaction was performed without the addition ofreverse transcriptase.

Construction of B. ovatus strains

In order to construct a strain of B. ovatus capable of expressing MuIL2in a xylan-inducible manner, the MuIL2 gene (minus native signalsequence) and 3′ portion of the orf gene of the xylanase operon werePCR-amplified and ligated in pGEM-T to give plasmid pORF-MuIL2. An ATGstart codon was positioned before the sequence encoding the mature MuIL2as part of an Ndel site. This ensured translation of the protein. Theuse of this Ndel site for cloning resulted in a single base change (G toA) in the non-coding region between off and the MuIL2 gene compared tothe wild-type region between off and xyl. However, this was not expectedto affect MuIL2 expression. The construction of plasmid pBOMuIL2 in FIG.1 comprises the 3′ portion of the B. ovatus off gene and entire MuIL 2gene amplified by PCR, ligated together in pBluescript then subclonedinto pBT2 to create pBOMuIL2. Only restriction sites used for cloningare shown in the Figure. tet, tetracycline resistance for selection inB. ovatus; kan, kanamycin resistance for selection in E. coli; oriV,origin of replication; repA, repB, repC encode replication functions andmob is required for mobilization from E. coli to B. ovatus. The pBOMuIL2plasmid (FIG. 1) was then successfully transferred to B. ovatus V975.The MuIL2-secreting strain, B. ovatus BOMuIL2-S, was constructed in thesame way except that the forward primer used to PCR-amplify the MuIL2gene, contained the sequence coding for the B. fragilis enterotoxinsecretion signal sequence. A control strain, B. ovatus BT2 was alsoconstructed by cloning only the off gene into pBT2. Successfulconstruction of the MuIL2 and MulL2-S expression strains, and BT2control strain was confirmed by PCR and nucleotide sequencing (data notshown).

EXAMPLE 1

A study was undertaken to assess the ability to colonise the mouseintestine of the genetically engineered strain of B. ovatus, B.ovatus-MuIL2, designed to produce the murine growth factor Interleukin-2(IL-2) in the presence of xylan.

Since the utility of using B.ovatus-MuIL2 to treat IL2^(−/−) mice isdependent upon demonstrating that it can colonise the mouse colon, wedetermined if B.ovatus-MuIL2 could colonise the colon of wildtype mice.Wildtype, specific pathogen free (SPF), C57BL/6 mice, maintained on aconventional diet (containing xylan), were infected with a singleinoculum of ˜10¹⁰ cfu B.ovatus-MuIL2 by oral gavage. Colonisation wasevaluated 7, 14, 21 and 28 days later by culturing faecal pellets underanaerobic conditions in the presence of antibiotics permissive for thegrowth of all Bacteroides sp., or for the growth of B.ovatus-MuIL2alone. In future experiments the identity of B.ovatus-MuIL2 in faecalcultures will be more extensively verified by colony filterhybridisation techniques using a full-length murine IL2 cDNA clone as aprobe. As shown in Table 1, B.ovatus-MuIL2 was present in faecal pelletsof 3/5 animals up to 28 days post inoculation, consistent with theirability to at least transiently colonise the mouse colon. The colons ofanimals 2, 3 and 5 analysed at 28 days post inoculation contained largenumbers (2-8×10⁷ cfu/g which theoretically could produce 20-80 μg MuIL2)of B. ovatus-MuIL2, consistent with faecal bacteria counts. By contrast,the colons of mice No. 1 and 4 contained no B. ovatus-MuIL2 consistentwith colonisation failure. The efficiency and duration of colonisationcould be improved by increasing the number of bacteria in the infectiveinoculum, or by repeated administration of bacteria.

TABLE 1 Faecal anaerobic bacteria counts from mice “infected” with B.ovatus-MuIL2 Total Bacteroides (×10⁸ cfu/g) B. ovatus-MuIL2 (×10⁴ cfu/g)Mouse T0 T7 T14 T21 T28 T0 T7 T14 T21 T28 1 12 1.6 7.5 5.4 5.8 — nd ndnd nd 2 17 3.6 4.8 2.9 8.3 — 0.67 2.74 5.4 10.1 3 15 4.1 3.7 3.5 3.7 —0.53 3.2 4.9 9.3 4 18 7.8 1.1 6.0 1.3 — nd nd nd nd 5 13 5.1 2.5 7.0 3.4— 0.21 4.61 7.9 12.2 nd, Not detectable.

EXAMPLE 2

A study was undertaken to assess the ability of the geneticallyengineered strain of B. ovatus, B. ovatus-MulL2, designed to produce themurine growth factor lnterleukin-2 (IL-2) in the presence of xylan toadversely affect the onset or severity of intestinal inflammation thatspontaneously occurs in mice genetically deficient of IL-2 (IL-2^(−/−)mice). A

concern in using commensal bacteria in immunotherapy protocols for IBDis that the chosen bacteria may, in immunocompromised animals andpatients, be “pathogenic” and promote, amplify or sustain intestinalinflammation. Bacteroides, and in particular B. fragilis and B.vulgatis, have been associated with the development of intestinalinflammation in experimental animal models of IBD and in IBD patients.One study has also identified increased titres of IgA and IgG antibodiesreactive with antigens of B. ovatus in the sera of IBD patients⁵.However, it is not clear if this was a cause of intestinal inflammation,or was secondary to Bacteroides and other commensal bacteria gainingentry to the systemic circulation and triggering immune responses as aresult of damage to the epithelial barrier. In view of these findings wethought it necessary to determine if B. ovatus has any adverse effect onthe development of colitis in IL2^(−/−) mice, which would otherwiseconfound or counteract any potential benefit that treatment withB.ovatus-MuIL2 might have in these animals.

Two groups (n=6 ea.) of age and sex matched, 3 week old, colitis-freeSPF IL2^(−/−) mice maintained on a conventional diet were infected with˜10¹⁰ cfu B. ovatus (V975) in 200 μl of PBS, or PBS alone every 7 daysfor 6 weeks by which time untreated IL2^(−/−) mice have developed severedisease. At 3 and 6 weeks post-infection animals were euthanized andtissues (spleen, lymph node and colon) analysed grossly andhistologically for disease pathology. A validated histologicinflammatory score was used for blinded evaluation of intestinalinflammation.

Our findings indicate that B. ovatus neither accelerates the onset norincreases the severity of colitis that normally develops in IL2^(−/−)mice. This gross and histological evaluation does not, however, excludethe possibility of there being other, more subtle, changes in forexample, the number, distribution and/or activity of immune cells in thetissues and colon of animals treated with B. ovatus. More detailedimmunological analyses will therefore, be carried out.

EXAMPLE 3

To assess the production of MuIL2 by strains BOMuIL2 and BOMuIL2-S,recombinant strains (BOMuIL2, BOMuIL2-S and BT2) and the wild typestrain (V975) were grown in medium with or without xylan. In addition,BOMuIL2 and BOMuIL2-S were grown for 16 h without xylan (RGM withglucose) followed by a further 8 h with xylan to demonstrate theinducible nature of production. Cell lysates and culture supernatantswere assayed for MuIL2 by ELISA and bioassay. Representative resultsfrom 3 independent experiments are shown in FIG. 2, levels of MuIL2 incell lysates (CL) and culture supernatants (SN) of B. ovatus BOMuIL2, B.ovatus BOMuIL2-S and control strains (V975 and BT2) grown with xylan for24 h (+X) or without xylan. BOMuIL2-S was also grown without xylan for16 h followed by 8 h with xylan (+X8). Test and control strains of B.ovatus were grown in RGM with or without xylan. Cells were harvested andlysed and the amount of MuIL2 in lysates and culture supernatantsdetermined by ELISA. MuIL2 was quantified by comparison to a dilutionseries of recombinant MuIL2. Data points are mean +/− standard error.MuIL2 was detected in the cell lysate of B. ovatus BOMuIL2 grown withxylan (539.5 pg ml⁻¹) and at a lower concentration (44.2 pg ml⁻¹) inculture supernatants. For strain BOMuIL2-S, 19.3 times more MuIL2 (849.9pg ml⁻¹) was detected in the supernatant of the culture grown in thepresence of xylan compared to BOMuIL2. A lower concentration of MuIL2(184.3 pg ml⁻1) was detected in the cell lysate of BOMuIL2-S. MuIL2 wasnot detected in cell lysates or culture supernatants from the twocontrol strains or from B. ovatus BOMuIL2 or BOMuIL2-S cultured in theabsence of xylan.

EXAMPLE 4

An IL2 bioassay demonstrated that the MuIL2 produced by BOMuIL2-S wasbiologically active (FIG. 3). FIG. 3 shows the results of a bioassay ofMuIL2 in culture supernatants of B. ovatus BOMuIL2-S grown with xylan.Proliferation of CTLL-2 cells was measured by the uptake of[³H]thymidine following incubation with doubling dilutions of:▪, B.ovatus BOMuIL2-S supernatant alone; □, B. ovatus BOMuIL2-S supernatantwith anti-MuIL2 antibody. MuIL2 was quantified by comparison to adilution series of recombinant MuIL2. Data points are mean +/− standarderror. Biological activity was not detected in supernatants from thecontrol strains or culture medium alone (data not shown). The blockingof proliferation of the indicator cell line by the addition of ananti-MuIL2 antibody demonstrated that the growth promoting activity inculture supernatants of B. ovatus pBOMuIL2-S was due to MuIL2. In strainBOMuIL2-S, an ATG codon was added to the 5′ end of the MuIL2 gene inorder to facilitate translation. Consequently, a methionine residue waspresent on the N-terminus of the mature protein. The results of thebioassay demonstrated that this did not ablate the biological activityof the protein. Likewise, secretion of MuIL2 directed by the B. fragilisenterotoxin secretion signal sequence did not eliminate the biologicalactivity of MuIL2. The higher concentrations of cell lysates andsupernatants proved inhibitory to the indicator cell line hence thelower concentration of MuIL2 measured in the 1/40 dilution of BOMuIL2-Ssupernatant.

EXAMPLE 5

To confirm transcription of the orf-MulL2 gene fusion, RT-PCR wasperformed. B. ovatus BOMuIL2 and BOMuIL2-S were grown in RGM withglucose for 16 h and a cell sample taken. Xylan was then added andsamples taken after 1 h. Samples from cultures of control strains werealso taken following xylan induction. Total RNA was extracted from cellsand RT-PCR performed with primers specific for the orf-MuIL2 constructand for gyrA, a commonly used constitutively expressed control gene. Abasal level of transcription could be detected in both BOMuIL2 andBOMuIL2-S strains before addition of xylan that increased 1 h afterxylan addition (FIG. 4). FIG. 4 shows increased expression of MuIL2 mRNAin response to xylan as determined by RT-PCR. Test (BOMuIL2 andBOMuIL2-S) or control strains (V975 and BT2) of B. ovatus which weregrown for 24 h in RGM without xylan. Xylan was then added and incubationcontinued for 1 h. Cells were harvested, total RNA extracted and RT-PCRperformed to detect MuIL2 and MuIL2-S transcripts. gyrA was used as apositive control. Lanes: 1, V975 grown with xylan for 1 h; 2, BT2 grownwith xylan for 1 h; 3, BOMuIL2 grown without xylan; 4, BOMuIL2 grownwith xylan for 1 h; 5, BOMuIL2-S grown without xylan; 6, BOMuIL2-S grownwith xylan for 1 h.

MuIL2 gene transcription was not detected in the two control strains.Although transcription was detected in the MuIL2-producing strainsbefore the addition of xylan, it was not possible to detect the MuIL2protein in cell lysates or culture supernatants (FIG. 2).

The data presented herein demonstrates that biologically active MuIL2can be produced under strict regulation of the xylanase operon in B.ovatus, a member of the resident gut microflora. Furthermore,biologically active MuIL2 could also be secreted by B. ovatus byincorporating the B. fragilis enterotoxin secretion signal sequence. Thelevel of MuIL2 in the culture supernatant of strain BOMuIL2 wasrelatively low but was increased 19.3 fold by the addition of thesecretion signal sequence (strain BOMuIL2-S). The xylanase operon hasbeen advantageously utilised for regulated gene expression by virtue ofthe inducible nature of this operon in the presence of xylan. Althoughthe promoter of this operon has not been cloned or characterized, theactivity of enzymes encoded by genes in the operon have been shown to beupregulated in response to xylan. The system of the present inventionalso provides for the control or regulation in vivo by dietary intake ofxylan. This feature of the invention has the advantage over otherinducible systems in that xylan remains undigested as it passes throughthe gut to the colon and is only degraded in the colon by the action ofmicrobial enzymes.

Although a basal level of transcription was detected in cells grownwithout xylan, MuIL2 production was at a level too low (<20 pg ml⁻¹) fordetection by ELISA in cell lysates or culture supernatants. Theinability to detect any MuIL2 in xylan-induced cultures of B. ovatuspBOMuIL2 following withdrawal of xylan demonstrated the stringency ofthe xylanase operon and a need for the continued presence of xylan forMuIL2 production (data not shown). The levels of MuIL2 produced andsecreted by B. ovatus are low, but within physiological range. This iscrucial if this system is to be used therapeutically as enough MuIL2must be produced to have a biological effect but levels must not be sogreat as to have a detrimental effect. We now intend to test theMuIL2-producing and secreting strains of B. ovatus in mouse models ofIBD to determine their ability to treat and prevent disease.

EXAMPLE 6

Adult C57BL/6 mice were administered a single dose of recombinant strainof B. ovatus expressing the murine IL2 gene by oral gavage (10⁸ cfu inPBS) and 3 and 7 days (T) later the stools were cultured for thepresence of all native Bacteroides sp. and the recombinant B. ovatususing selective culture conditions and use of antibiotics. Bacteriacolonies (cfu) were quantitated after 24 h.

The results show that recombinant B. ovatus strain colonises the colonof the majority (4/5) of mice for up to one week after a single dose ofbacteria. The presence of the recombinant B. ovatus has no discernableimpact on the size of the endogenous populations of Bacteroides.

TABLE 2 Colonisation of mice by recombinant strains of B. ovatusRecombinant Total Bacteroides cfu g⁻¹ B. ovatus cfu g⁻¹ Mouse T0 T3 T7T0 T3 T7 1 1.16 × 10⁹ 1.61 × 10⁹ 7.54 × 10⁸ — 1208 1555 2 1.66 × 10⁹3.61 × 10⁸ 4.75 × 10⁸ — 997 1054 3 1.50 × 10⁹ 4.06 × 10⁸ 3.73 × 10⁸ —5263 5409 4 3.81 × 10⁹ 7.77 × 10⁸ 1.08 × 10⁹ — 0 0 5 1.32 × 10⁹ 5.05 ×10⁸ 2.50 × 10⁸ — 2105 1636

EXAMPLE 7

FIG. 5 shows the construct map of B ovatus expressing either human TGFβor KGF. Recombinant strains of B.ovatus expressing genes encoding eitherhuman KGF (BoHuKGF) or TGFβ (BoHuTGF) or, control strains (BOBTS) thatcontain no heterologous genes were cultured in complete media alone(Media) or in media containing xylan for 8 or 24 h prior to assayingculture supernatants for TGFβ and KGF by ELISA. Some cultures ofrecombinant B.ovatus were cultured with xylan for 8 h prior to removingmedia and culturing for a further 24 h in complete media alone(BoHuKGF/TGF±xylan). FIG. 6A shows the graphs of the average amounts(±SEM) of cytokine present in the culture supernatants detected in 3independent experiments with B.ovatus expressing the gene encoding humanKGF TGFβ (BoHuTGF). FIG. 6B shows the same experimental data from B.ovatus expressing the gene encoding human KFG (BoHuKGF).

In summary, the ability to engineer commensal bacteria to produceimmunomodulatory molecules under the control of dietary factors, ashereinbefore described, offers the potential of providing a moremeasured, specific arid controlled therapy for chronic gut disorderssuch as IBD. This approach can be used to deliver a variety ofbiologically relevant molecules, including cytokines, enzymes andvaccines, with applications in treatment and prevention of a variety ofdisorders.

REFERENCES

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1. A recombinant Bacteroides ovatus gut commensal bacterium deposited atthe National Collection of Industrial, Food and Marine Bacteria (NCIMB)Accession No. 41521, 41522 or 41523 wherein the bacterium comprises axylanase promoter that regulates expression of a polypeptide or proteinand wherein the promoter is induced in the presence of dietary xylan. 2.The bacterium of claim 1, wherein the bacterium is non-pathogenic toman.
 3. The bacterium of claim 1, wherein the polypeptide or protein isselected from the group consisting of insulin, growth hormone,prolactin, calcitonin, luteinizing hormone, parathyroid hormone,somatostatin, thyroid stimulating hormone, vaccines, antigens,vasoactive intestinal polypeptide, trefoil factors, cell and tissuerepair factors, transforming growth factor β, keratinocyte growthfactor, a structural group 1 cytokine adopting an antiparallel 4αhelical bundle selected from the group consisting of IL-2, IL-3, IL-4,IL-5, IL-6, IL-7, IL-9, IL-10, IL-11, IL-12, IL-13, GM-CSF, M-CSF, SCF,IFN-γ, EPO, G-CSF, LIF, OSM, CNTF, GH, PRL or IFNα/β, a structural group2 cytokine selected from the group consisting of TNFα, TNFβ, CD40, CD27or FAS ligands, IL-1 family of cytokines, fibroblast growth factorfamily, platelet derived growth factors, transforming growth factor βand nerve growth factors, a structural group 3 cytokine, epidermalgrowth factor family of cytokines, chemokines, insulin relatedcytokines, and a structural group 4 cytokine selected from the groupconsisting of EGF, immunoglobulin-like and kringle domains.
 4. Thebacterium of claim 1, wherein the bacterium of NCIMB Accession No.41521, 41522 or 41523 expresses a plurality of polypeptides or proteins.5. A pharmaceutical composition comprising: (a) a recombinantBacteroides ovatus gut commensal bacterium deposited at the NationalCollection of Industrial, Food and Marine Bacteria (NCIMB) Accession No.41521, 41522 or 41523 wherein the bacterium comprises a xylanasepromoter that regulates expression of a polypeptide or protein andwherein the promoter is induced in the presence of dietary xylan; and(b) a pharmaceutically acceptable carrier, diluent or excipient.
 6. Amethod of treating chronic inflammatory bowel disease comprisingadministering to a subject in need thereof an effective amount of arecombinant Bacteroides ovatus gut commensal bacterium deposited at theNational Collection of Industrial, Food and Marine Bacteria (NCIMB)Accession No. 41521, 41522 or 41523 wherein the bacterium comprises axylanase promoter that regulates expression of a polypeptide or proteinand wherein the promoter is induced in the presence of dietary xylan. 7.A method of treating chronic inflammation of the gut comprisingadministering to a subject in need thereof an effective amount of arecombinant Bacteroides ovatus gut commensal bacterium deposited at theNational Collection of Industrial, Food and Marine Bacteria (NCIMB)Accession No. 41521, 41522 or 41523 wherein the bacterium comprises axylanase promoter that regulates expression of a polypetide or proteinand wherein the promoter is induced in the presence of dietary xylan. 8.The bacterium of claim 1, wherein polypeptide or protein is obtainedfrom a eukaryotic, prokaryotic or viral source.
 9. The recombinantBacteroides ovatus gut commensal bacterium of claim 1, wherein thebacterium further comprises a Bacteroides fragilis endotoxin secretionsignal sequence to mediate secretion of the Polypeptide or protein. 10.The pharmaceutical composition of claim 5, wherein the bacterium furthercomprises a Bacteroides fragilis endotoxin secretion signal sequence tomediate secretion of the polypeptide or protein.
 11. The method of claim6, wherein the bacterium further comprises a Bacteroides fragilisendotoxin secretion signal sequence to mediate secretion of thepolypeptide or protein.
 12. The method of claim 7, wherein the bacteriumfurther comprises a Bacteroides fragilis endotoxin secretion signalsequence to mediate secretion of the polypeptide or protein.